Manganese in PDB 6a4f: Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H

The structure of Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H, PDB code: 6a4f was solved by C.W.Lee, S.Park, J.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.02 / 2.21
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.285, 59.285, 234.160, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 27

The binding sites of Manganese atom in the Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H (pdb code 6a4f). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H, PDB code: 6a4f:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:75.8 occ:1.00 O2P A:U5P201 2.2 58.3 1.0 OD1 A:ASP12 2.2 32.2 1.0 O3' A:U5P202 2.5 54.6 1.0 CG A:ASP12 3.2 40.0 1.0 P A:U5P201 3.3 53.9 1.0 OD2 A:ASP12 3.5 38.9 1.0 O1P A:U5P201 3.6 64.2 1.0 O A:HOH341 3.7 41.5 1.0 O5' A:U5P201 3.8 56.7 1.0 C3' A:U5P202 3.9 80.0 1.0 O A:LEU13 4.0 36.4 1.0 C5' A:U5P201 4.0 57.0 1.0 OD2 A:ASP112 4.0 44.0 1.0 O A:HOH347 4.3 48.8 1.0 OD2 A:ASP163 4.3 45.7 1.0 O A:HOH332 4.4 40.9 1.0 OD1 A:ASP112 4.4 46.1 1.0 C4' A:U5P202 4.6 71.8 1.0 O3P A:U5P201 4.6 64.5 1.0 CB A:ASP12 4.6 32.6 1.0 CG A:ASP112 4.7 39.6 1.0 O A:ASN107 4.7 36.3 1.0 N A:LEU13 4.9 36.3 1.0 O2' A:U5P202 4.9 84.9 1.0 C5' A:U5P202 4.9 67.2 1.0

Manganese binding site 2 out of 2 in the Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Separated Uridine Bound Oligoribonuclease (Orn) From Colwellia Psychrerythraea Strain 34H within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:91.1 occ:1.00 OD1 B:ASP12 2.1 62.9 1.0 O3P B:U5P201 2.3 67.9 1.0 O B:HOH301 2.3 51.3 1.0 O B:HOH355 2.4 56.5 1.0 O B:HOH302 2.6 59.1 1.0 CG B:ASP12 3.1 65.8 1.0 O3' B:U5P202 3.4 0.7 1.0 P B:U5P201 3.4 70.1 1.0 OD2 B:ASP12 3.5 67.1 1.0 C3' B:U5P202 3.5 0.6 1.0 O1P B:U5P201 3.5 77.9 1.0 O B:HOH353 3.9 61.5 1.0 O B:LEU13 4.0 51.5 1.0 O5' B:U5P201 4.1 72.8 1.0 C5' B:U5P201 4.1 70.9 1.0 OD2 B:ASP112 4.1 75.4 1.0 O B:HOH350 4.2 53.3 1.0 OD1 B:ASP112 4.3 62.5 1.0 O B:ASN107 4.4 47.2 1.0 C4' B:U5P202 4.4 96.9 1.0 CB B:ASP12 4.4 66.4 1.0 OD2 B:ASP163 4.4 84.5 1.0 C5' B:U5P202 4.6 82.3 1.0 CG B:ASP112 4.6 59.5 1.0 C2' B:U5P202 4.8 1.0 1.0 O2P B:U5P201 4.8 73.2 1.0 N B:LEU13 4.8 66.5 1.0 CA B:ASP12 4.9 61.5 1.0 OE2 B:GLU14 4.9 76.7 1.0

C.W.Lee, S.H.Park, C.S.Jeong, S.S.Cha, H.Park, J.H.Lee. Structural Basis of Small Rna Hydrolysis By Oligoribonuclease (Cpsorn) From Colwellia Psychrerythraea Strain 34H. Sci Rep V. 9 2649 2019.
ISSN: ESSN 2045-2322
PubMed: 30804410
DOI: 10.1038/S41598-019-39641-0